In terms of aikido, I also understand that shuriken were, at one time, taught at the Iwama dojo, but the practice was mostly discontinued some years ago.

A friend of mine who recently returned from being an uchideshi at Iwama said that he was taught shurikenjutsu (using the spike type shuriken) from Saito sensei (both the late Morihiro Saito sensei as well as Hitohiro Saito sensei). It's not a "regular" part of practice, but it hasn't been discontinued, per se.